Regulatory structures of gene expression, DNA-replication and DNA-rearrangement in macronuclear genes of Stylonychia lemnae, a hypotrichous ciliate

Helftenbein, Elke; Conzelmann, Karl‐Klaus; Becker, Karl‐Friedrich; Fritzenschaf, H.

doi:10.1016/s0932-4739(89)80026-4

Cited by 17 publications

(5 citation statements)

References 49 publications

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“…This is also the case for the Paramecium 3-tubulin gene where the average G+C content is 14% in intron sequences, against 42 % in the adjacent coding sequences. These figures, similar to those found in Tetrahymena, may reflect a property of ciliate genomes to present a particularly high proportion of A and T in noncoding sequences (Horowitz et al, 1987;Helftenbein et al, 1989;P.Dupuis, unpublished results). In plants (Goodall and Fillipowicz, 1989), the abundance of A+T in introns, either because it reduces potential secondary structure, or because they act as a recognition signal for hnRNP, is absolutely Figure 5a).…”

Section: Resultssupporting

confidence: 76%

The beta-tubulin genes of Paramecium are interrupted by two 27 bp introns.

Dupuis

1992

The EMBO Journal

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In the ciliate Paramecium tetraurelia, the analysis of the tubulin gene family has revealed the existence of four a and three 3 genes. We show here that the coding sequence of the first (3-tubulin gene to be cloned and sequenced is interrupted by two short non-coding sequences of 27 bp each, which present at their extremities the pairs GT/AG, characteristic of eukaryotic pre-mRNA introns, and the internal pentanucleotide TTAAT, consensual inTetrahymena introns. We demonstrate by PCR experiments that the three macronuclear ,B-tubulin genes contain these sequences in similar positions, thereby ruling out the possibility that these sequences are ciliate IES present in the micronucleus and eliminated in the transcriptionally active macronucleus. Si mapping analysis and mRNA sequencing show that the sequences are absent from the j-tubulin transcripts. These sequences are the first introns described in protein encoding genes in P.tetraurelia and the shortest known introns altogether.

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Section: Resultssupporting

confidence: 76%

The beta-tubulin genes of Paramecium are interrupted by two 27 bp introns.

Dupuis

1992

The EMBO Journal

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“…Currently we do not have a clear explanation for this strand-nonsensitive oscillation in the subtelomeric regions. Considering the special location of the subtelomeric regions, they may serve regulatory and structural functions for chromosome fragmentation, addition of telomeres, and initiation of transcription and replication ( Helftenbein et al. 1989 ; Prescott 1994 ; Johnson et al.…”

Section: Resultsmentioning

confidence: 99%

Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina

Zhang

Wang

Yan

et al. 2018

Genome Biology and Evolution

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Ciliated protists are a large group of single-celled eukaryotes with separate germline and somatic nuclei in each cell. The somatic genome is developed from the zygotic nucleus through a series of chromosomal rearrangements, including fragmentation, DNA elimination, de novo telomere addition, and DNA amplification. This unique feature makes them perfect models for research in genome biology and evolution. However, genomic research of ciliates has been limited to a few species, owing to problems with DNA contamination and obstacles in cultivation. Here, we introduce a method combining telomere-primer PCR amplification and high-throughput sequencing, which can reduce DNA contamination and obtain genomic data efficiently. Based on this method, we report a draft somatic genome of a multimacronuclear ciliate, Uroleptopsis citrina. 1) The telomeric sequence in U. citrina is confirmed to be C4A4C4A4C4 by directly blunt-end cloning. 2) Genomic analysis of the resulting chromosomes shows a “one-gene one-chromosome” pattern, with a small number of multiple-gene chromosomes. 3) Amino acid usage is analyzed, and reassignment of stop codons is confirmed. 4) Chromosomal analysis shows an obvious asymmetrical GC skew and high bias between A and T in the subtelomeric regions of the sense-strand, with the detection of an 11-bp high AT motif region in the 3′ subtelomeric region. 5) The subtelomeric sequence also has an obvious 40 nt strand oscillation of nucleotide ratio. 6) In the 5′ subtelomeric region of the coding strand, the distribution of potential TATA-box regions is illustrated, which accumulate between 30 and 50 nt. This work provides a valuable reference for genomic research and furthers our understanding of the dynamic nature of unicellular eukaryotic genomes.

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“…From these data it is obvious that the subtelomeric regions of the macronuclear gene-sized DNA molecules show a common se- T h e two subtelomeric regions of gene-sized DNA molecules were analyzed for the presence of direct repeats, inverted repeats, consensus sequences and palindromic sequences. The table is subdivided into seven columns (left to right): DNA molecule and standard primer used for sequence analysis, inverted repeats at positions 1-10 (since sequences are always presented in 5'-3' direction inverted repeats appear as direct repeats in the table), perfect inverted repeats a t approximately position 40 (the positions in the two subtelomeric regions are given in brackets), sequences resembling the consensus sequence at approximately position 60 (nucleotides identical to the consensus sequence are written in large letters, palindromic nucleotides are written in bold letters), palindromic sequences at approximately position 60 (palindromic nucleotides are written in bold letters), GC-content and G-content of both subtelomeric regions, size of the DNA molecule'-', cyI-and a,-tubulin genes (Helftenbein, 1985;Helftenbein et al, 1989);3-4, p2and p,-tubulin genes (Conzelmann and Helftenbein, 1986;;5, calmodulin gene (Gaunitz et al, 1992); , ribosomal RNA gene (G. Steinbriick, personal comm~nication);~-", 1.0 and 1.4 kb macronuclear DNA molecule (Eder et al, in p r e~s ) ;~: histone H4 gene (Wefes and Lipps, 1990);lo, macronuclear DNA molecule Ma91 (P. Richter, personal communication);", overamplified bend gene (Wegner et al, 1989);12, T-complex protein 1 gene (C. Maercker, personal communication);'3, elongation factor l a gene (Bierbaum et al, 1991);14, ladder gene (H. Fritzenschaf, personal communication);'"'", telomere binding proteins (Fang and Cech, 1991);17, 2.6-kb macronuclear DNA molecule (Stoll et al, 1993).…”

Section: Resultsmentioning

confidence: 99%

Analysis of the subtelomeric regions of macronuclear gene‐sized DNA molecules of the hypotrichous ciliate Stylonychia lemnae: Implications for the DNA fragmentation process during macronuclear development?

Maercker

Lipps

1993

Dev. Genet.

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The subtelomeric regions of macronuclear gene-sized DNA molecules from Stylonychia lemnae were analyzed. The results obtained indicate that these regions show a highly ordered and common sequence organization: Immediately adjacent to the telomeric sequence a short inverted repeat sequence is found, followed by another 7-9 bp inverted repeat sequence at approximately position 40. A 10 bp consensus sequence found in the subtelomeric regions of all gene-sized DNA molecules is found at approximately position 60 and in addition at about the same position palindromic sequences showing no homology to each other are localized. The biological significance of this sequence organization is discussed.

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Regulatory structures of gene expression, DNA-replication and DNA-rearrangement in macronuclear genes of Stylonychia lemnae, a hypotrichous ciliate

Cited by 17 publications

References 49 publications

The beta-tubulin genes of Paramecium are interrupted by two 27 bp introns.

The beta-tubulin genes of Paramecium are interrupted by two 27 bp introns.

Insights into an Extensively Fragmented Eukaryotic Genome: De Novo Genome Sequencing of the Multinuclear Ciliate Uroleptopsis citrina

Analysis of the subtelomeric regions of macronuclear gene‐sized DNA molecules of the hypotrichous ciliate Stylonychia lemnae: Implications for the DNA fragmentation process during macronuclear development?

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